Dozens of UFOs suddenly appear on Earth, hovering over major cities around the world and claim that their objective is to help the Human race, providing vastly superior intelligence and technology in exchange for water and minerals only found on Earth. The leader of the Vs, Anna, uses popular TV anchor Chad Decker to deliver her messages to the Humans, but suspicion arises from FBI investigator Erica who believes that the Vs have different intentions to what they claim.

Chad Decker hosts a debate about the Vs. Suspicion arises from FBI investigator Erica who believes that the Vs have different intentions to what they claim. Erica and Father Jack find themselves being tracked down by a seeker.

Erica works with new allies to uncover a biological threat they suspect the Visitors have been plotting. Aboard the mothership, Anna meets with a special guest, while managing the investigation into the murder of a V. Chad does a segment on the V Healing Centers demonstrating their amazing medical abilities, but finds himself conflicted by some of his findings.

Erica finds her life in danger when she's attacked at home. A dangerous new member is recruited for the Resistance as the Visitors shore up their defenses. Anna wonders why Chad hasn't followed up on his diagnosed aneurysm and Ryan's concern grows over Val's "abnormal" pregnancy.

Erica, Ryan, Father Jack and Hobbes learn Anna's sent a V shuttle filled with a deadly tracker team to find them, and must figure out how to stop the shuttle from landing. Meanwhile, Anna gives Tyler his invitation to the Live Aboard Program and Chad confronts Father Jack on what he knows about The Fifth Column.

After a violent attack on someone very close to Anna, she delivers a message that the Vs don't feel safe and will be leaving, while she also gives a list of possible Fifth Column members to Chad hoping he'll investigate to help in finding them. Meanwhile, Erica and the team try to track down a scientist who may have created a weapon that the Visitors are afraid of.

A V soldier is still on the hunt for Val when her water breaks and her baby will soon be born. Meanwhile, Erica, tired of being on the defensive, decides to go on the offensive and gets herself and Tyler invited up to the Mothership for a get-to-know-everyone-better dinner. But she has more than food on her mind; she's really there to find Anna's soldiers and destroy them. Meanwhile, after Father Jack asks Chad to help get a message to Joshua, he discovers that Anna's been using him.

The Season Two opener, "Red Rain," continues the action from last season's finale when Anna unleashed Red Sky on the planet. With the world on the brink of war and chaos all around, is there anyone who can stand up to Anna? Meanwhile, Ryan has been kept in isolation on the mothership, away from his hybrid baby so that Anna can experiment on her. Chad, seeking redemption for being used by Anna, now wants to fight with the Fifth Column, and Erica goes on a journey to find a scientist who can give her the answers to what Red Sky is, and where she learns the horrifying secret of what the Vs are doing on our planet.

After the radical faction of the Fifth Column murders three Peace Ambassadors, Erica goes on a mission to hunt down their leader, Eli Cohn, a former Mossad agent. Meanwhile, as Jack and other priests around the globe begin to speak out against the Visitors, Anna heads to the Vatican in an effort to convince the leaders of organized religion that the Visitors truly are "of peace".

Anna uses her newest gift to mankind, "Concordia," as a cover to hide an invading fleet of breeding vessels that will be used to ensure the perpetuation of Visitors for future generations. Meanwhile, Eli Cohn (guest star Oded Fehr) tries to convince Erica and the Fifth Column that the "Concordia" gala is the perfect time to assassinate Anna.

Anna, enraged at the increasing audacity of the Fifth Column attacks, enlists Ryan in an attempt to wipe out the Fifth Column in one fell swoop. Meanwhile, Father Travis, following Vatican orders, asks Jack to leave the church, and Lisa meets Diana, her grandmother – who Anna said was dead – for the first time.